Contacts of the strand formed by residues 104 - 108 (chain F) in PDB entry 5MGT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 104 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94F CYS* 4.5 0.2 - - - -
99F GLN 3.8 0.2 - - - +
100F GLN* 3.4 5.7 - - - +
101F LEU* 2.8 36.7 + - + +
102F ARG 3.5 0.2 - - - -
103F GLU* 1.3 78.6 - - - +
105F CYS* 1.3 63.5 - - - +
106F LEU* 4.2 16.8 - - + -
130F LEU* 4.5 0.2 - - - +
131F LEU* 2.5 32.7 + - - +
133F ARG* 3.7 27.7 - - - +
137F GLU* 2.6 25.0 + - - +
211F GLN* 2.8 38.2 + - + +
212F LYS 3.5 7.9 - - - +
213F GLU* 3.6 18.4 - - - +
214F LEU* 4.6 0.9 - - - -
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Residues in contact with CYS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LEU* 3.9 9.4 - - - -
94F CYS* 2.1 54.3 - - + -
95F PRO* 4.6 1.3 - - + -
98F TRP* 3.6 16.5 - - + -
99F GLN 3.4 4.9 - - - -
104F LYS* 1.3 73.7 - - - +
106F LEU* 1.3 61.3 + - - +
211F GLN* 3.1 7.4 - - - +
212F LYS* 2.8 40.1 + - + +
214F LEU* 3.6 23.6 - - - -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F TYR 4.5 0.2 - - - +
98F TRP* 3.4 6.7 - - - -
99F GLN* 2.8 40.7 + - + +
101F LEU* 4.2 18.8 - - + -
104F LYS* 4.2 13.0 - - + -
105F CYS* 1.3 81.5 - - - +
107F LEU* 1.3 59.5 + - - +
108F PHE* 3.8 24.3 + - + -
130F LEU* 3.8 25.4 - - + -
141F THR* 4.1 17.7 - - + +
144F LEU* 4.0 25.1 - - + -
209F ILE* 4.4 3.8 - - + -
210F CYS 3.2 4.5 - - - +
211F GLN* 3.9 11.2 - - + -
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Residues in contact with LEU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F TYR* 3.6 37.2 - - + +
98F TRP* 3.7 34.5 - - + +
106F LEU* 1.3 73.0 - - - +
108F PHE* 1.3 71.3 + - - +
109F SER* 3.7 3.5 + - - +
110F HIS* 6.2 1.3 - - - +
121F ASP* 5.4 0.9 - - - +
125F LYS* 3.7 37.2 - - + -
208F TRP* 3.6 1.4 - - - +
209F ILE* 3.3 6.6 - - - -
210F CYS* 2.8 38.5 + - + +
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Residues in contact with PHE 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F GLN* 3.6 27.9 - - - +
106F LEU* 3.8 36.8 - - + -
107F LEU* 1.3 83.7 - - - +
109F SER* 1.3 66.9 + - - +
110F HIS* 3.8 15.8 + - + -
141F THR* 4.3 6.5 - - + -
144F LEU* 4.1 25.8 - - + -
145F ILE* 3.8 21.3 - - + -
146F ARG* 4.3 16.2 - - - +
152F PHE* 3.9 21.8 - + + -
208F TRP 3.8 3.6 - - - -
209F ILE* 3.5 33.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il